Mini bioinformatics project: PCA on genotypes

This repo contains the code from this video: https://youtu.be/-PCKK_nwFdA

If you somehow end up publishing a paper based on this type of project, you should cite this original paper it was inspired by: https://www.nature.com/articles/nature07331

Preview VCF on 42basepairs

• Preview variants
• Subsample variants

Download data files on the command line

# Download from 42basepairs
curl -O "https://42basepairs.com/download/s3/1000genomes/release/20110521/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz"

curl -O "https://42basepairs.com/download/s3/1000genomes/release/20110521/ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz.tbi"

curl -O "https://42basepairs.com/download/s3/1000genomes/release/20110521/phase1_integrated_calls.20101123.ALL.panel"

# or use "wget" instead of "curl -O" if you don't have curl.

Colab notebook:

https://colab.research.google.com/drive/1o24ZfqDoBEwvRSx_Br1u7edPPXLLx4w7?usp=sharing